Bottom Line:
Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation.The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21.Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation.

ABSTRACTEarly sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼ 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.

pone.0119730.g002: Results from GWAS for grilsing.Horizontal dotted line represents the genome-wide significant threshold.

Mentions:
Analysis for grilsing identified five markers with a genome-wide significant association (p < 1.29e-5 according to the Bonferroni threshold and p < 0.05 for the permutation method) with the trait as shown in Table 2. These markers (ESTNV_20578_482, ESTNV_36582_634, ESTNV_34243_316, GCR_cBin47052_Ctg1_234, ESTNV_15175_311) are located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, respectively (Fig. 2). The most significantly associated marker ESTNV_20578_482 is located within an E2F Transcription Factor (E2F) and nearby the CCR4-NOT transcription complex gene. The next most significant marker ESTNV_36582_634 is located within a malate dehydrogenase gene (MDH) and close to a UDP-glucose pyrophosphorylase gene (UGP). The next marker showing a significant association was ESTNV_34243_316, a SNP located within a PQ Loop Repeat Containing gene. The other two markers that showed a genome-wide significant association with grilsing were located in uncharacterized genes, as shown in Table 2.

pone.0119730.g002: Results from GWAS for grilsing.Horizontal dotted line represents the genome-wide significant threshold.

Mentions:
Analysis for grilsing identified five markers with a genome-wide significant association (p < 1.29e-5 according to the Bonferroni threshold and p < 0.05 for the permutation method) with the trait as shown in Table 2. These markers (ESTNV_20578_482, ESTNV_36582_634, ESTNV_34243_316, GCR_cBin47052_Ctg1_234, ESTNV_15175_311) are located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, respectively (Fig. 2). The most significantly associated marker ESTNV_20578_482 is located within an E2F Transcription Factor (E2F) and nearby the CCR4-NOT transcription complex gene. The next most significant marker ESTNV_36582_634 is located within a malate dehydrogenase gene (MDH) and close to a UDP-glucose pyrophosphorylase gene (UGP). The next marker showing a significant association was ESTNV_34243_316, a SNP located within a PQ Loop Repeat Containing gene. The other two markers that showed a genome-wide significant association with grilsing were located in uncharacterized genes, as shown in Table 2.

Bottom Line:
Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation.The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21.Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation.

ABSTRACTEarly sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼ 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.